MSIsensor-pro: fast, accurate and matched-normal-sample-free detection of microsatellite instability

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

ABSTRACT We developed MSIsensor-pro ( https://github.com/xjtu-omics/msisensor-pro ), an open-source single sample microsatellite instability (MSI) scoring method for research and clinical applications. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative sites selection method to enable MSI detection without matched normal samples. For samples of various sequencing depths and tumor purities, MSIsensor-pro significantly outperformed the current leading methods in terms of both accuracy and computational cost.

Authors 9

1. Peng Jia

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 70049 China

2. Xiaofei Yang

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   School of Computer science and Technology, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China

   School of Computer science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China

3. Li Guo

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   The School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 70049 China

   The School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 71009 China

4. Bowen Liu

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 70049 China

5. Jiadong Lin Aachen Leiden Institute of Advanced Computer Science

   Leiden University · Xi'an Jiaotong University

   Affiliation as printed

   Leiden Institute of Advanced Computer Science, Leiden University, Leiden, 2311 ZE, the Netherlands

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 70049 China

6. Hao Liang

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 70049 China

7. Jianyong Sun

   Xi'an Jiaotong University

   Affiliation as printed

   School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an 710049, China

   School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an 710049, China

8. Chengsheng Zhang

   First Affiliated Hospital of Xi'an Jiaotong University · The Jackson Laboratory for Genomic Medicine

   Affiliation as printed

   Precision Medicine Center, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 China

   The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA

   Precision Medicine Center, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 10061 China

9. Kai Ye corresponding

   First Affiliated Hospital of Xi'an Jiaotong University · Xi'an Jiaotong University

   Affiliation as printed

   Genome Institute, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049 China

   The School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China

   Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061 China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 70049 China

   The School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 71009 China